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Heroes are the people who do what has to be done, when it needs to be done, regardless of the consequences.
| 2024 | Fellow of the Singapore National Academy of Science, for innovative and fundamental contributions to database theory and computational biology | Limsoon Wong |
| 2024 | Pingat Bakti Setia, or Long Service Medal in English, for irreproachable character in 25+ years of service to the Government of Singapore and its associated organizations | Limsoon Wong |
| 2016 | 12th International Conference on Advanced Data Mining and Applications (ADMA2016) Best Paper Award | Qian Liu, Jinyan Li, Limsoon Wong, Kotagiri Ramamohanarao |
| 2014 | Pingat Pentadbiran Awam (Gangsa), or Public Administration Medal (Bronze) in English, for outstanding efficiency, competence, and industry | Limsoon Wong |
| 2014 | ICDT 2014 Test of Time Award | Peter Buneman, Val Tannen, Limsoon Wong |
| 2014 | Red Herring Top 100 Asia | Molecular Connections Private Limited |
| 2013 | Fellow of the ACM, for contributions to database theory and computational biology | Limsoon Wong |
| 2013 | BT-YES Bank survey of India's Best SMEs - Best SME for Innovation (Small). According to the survey, "... [it] is an outstanding company which has shown a sustained bend towards value, creating innovation ... and has positively altered Industry dynamics." | Molecular Connections Private Limited |
| 2009 | Indian Institute of Economic Studies' "Udyog Rattan Award" and "Award for Excellence" | Molecular Connections Private Limited |
| 2008 | ICICI-CNBC Emerging India Small Enterprise of the Year Award |
Molecular Connections Private Limited CNBC interview video |
| 2007 | Rated by ISI as the 49th hottest paper in computer science published in 2006 ("Exploiting Indirect Neighbours and Topological Weight to Predict Protein Function from Protein-Protein Interactions". Bioinformatics, 22:1623--1630, July 2006) | Hon Nian Chua, Wing-Kin Sung, Limsoon Wong |
| 2007 | Winner, Protein-Protein Subnetwork Challenge, the 2nd Dialogue for Reverse Engineering Assessments and Methods (DREAM) | Hon Nian Chua, Hugo Willy, Guimei Liu, Xiaoli Li, Limsoon Wong, See-Kiong Ng |
| 2006 | Singapore Youth Award Medal of Commendation | Limsoon Wong |
| 2006 | ICAAS Distinguished Service Award | Limsoon Wong |
| 2006 | Ranked among the top 10 "prominent social actors who powered transition of data mining research to bioinformatics research" in [Zhou et al, "Topic evolution and social interactions: How authors effect research", CIKM2006] | Limsoon Wong |
| 2005 | I2R Biannual Best Paper Award | Haiquan Li, Jinyan Li, Limsoon Wong, Mengling Feng, and Yap-Peng Tan |
| 2004 | Ranked among the top 50 "Best Nurturers of Computer Science Research" in Indian Institute of Science Report IISc-CSA-TR-2004-10 | Limsoon Wong |
| 2003 | Asian Innovation Award (Gold Award) | Jinyan Li, Huiqing Liu, Limsoon Wong, and Allen Yeoh |
| 2003 | I2R Quarterly Best Paper Award | Jinyan Li, Huiqing Liu, See-Kiong Ng, and Limsoon Wong |
| 2002 | LIT Quarterly Best Paper Award | Jinyan Li, Huiqing Liu, and Limsoon Wong |
| 1999 | Singapore Youth Award | Limsoon Wong |
| 1998 | Tan Kah Kee Young Inventors Award (Commendation Award) | Oliver Wu and Liu Hai |
| 1998 | National University of Singapore Staff Achievement Award | Limsoon Wong |
| 1998 | ASEAN Certificate of Achievements | Limsoon Wong |
| 1998 | KRDL Quarter Cup | Limsoon Wong |
| 1997 | National Academy of Science Young Scientist Award | Limsoon Wong |
| 1997 | Lee Kuan Yew Postdoctoral Fellowship | Zhang Louxin |
| 1997 | Tan Kah Kee Young Inventors Award (Gold Award) | Limsoon Wong |
| 1995 | Lee Kuan Yew Postdoctoral Fellowship | Limsoon Wong |
| 1995 | Morris and Dorothy Rubinoff Award | Limsoon Wong |